Though conflict was found among every method or set of characters used to reconstruct trees, the five groups defined by the ribosomal protein-based phylogenies were largely in agreement across the range of different reconstruction methods and genome characters.
We selected the phylogeny inferred from a concatenation of ribosomal proteins by ML (Stamatakis 2006) and Bayesian sampling (Drummond et al. 2006) because it was largely consistent with various other reconstruction methods using multiple sets of genome characters, it could be rooted, and its edges could be scaled to substitutions per site and a relaxed molecular clock (fig. 1).
Interestingly, the whole genome character of S. scitamineum is most similar to U. maydis which belongs to a separate genus.
Probabilistic models of genome character evolution have been further elaborated by integrating birth-death models in a phylogenetic context [ 7- 14, 6].
However, because of the highly dynamic evolution of the chloroplast genome, structural genomic characters provide little information on higher order relationships within the Trebouxiophyceae and on the monophyletic/nonmonophyletic status of this class.
Analysis of genomic characters in the context of a species phylogeny is a rich source of insight into genome evolution.
The main parts of this nuclear gene tree [14] have nevertheless been supported in later studies based on far more comprehensive alignments [e.g. 17] and genome level characters like retroposon insertion and indel differences [18] [20].
If the linkage group number of the mapped SNP did not correspond to the chromosome number in the genome, the characters following the second letter are formatted as LGN_numerals, such as euLG02_006 and hmLG09_605, where 'LG' is the abbreviation for linkage group.
Whole mitochondrial genomes provide not only more general genetic information than shorter sequences of individual genes such as the COI gene, but also sets of genome-level characters, such as the relative position of different genes, structural genomic features and compositional features [ 1, 2, 11, 12].
Gene arrangement, gene content, tRNA secondary structures, and changes in genetic code are all mitochondrial genome-level characters, used to clarify some controversial phylogenetic relationships, especially at high taxonomic levels.
For each position in the reference genome, a binary character records whether the k-mer starting at this position is present ('1') or absent ('0') in the donor reads.
